X3DNA-DSSR Homepage -- Nucleic Acid Structures

Cover images provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

See the 2020 paper titled "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL" in Nucleic Acids Research and the corresponding Supplemental PDF for details. Many thanks to Drs. Wilma Olson and Cathy Lawson for their help in the preparation of the illustrations.

Details on how to reproduce the cover images are available on the 3DNA Forum.

November 2025

Structure of the human minor spliceosome pre-B complex (PDB id: 8Y7E; Bai R, Yuan M, Zhang P, Luo T, Shi Y, Wan R. 2024. Structural basis of U12-type intron engagement by the fully assembled human minor spliceosome. Science 383: 1245–1252). The protein–RNA assembly reveals the mechanisms of recognition and recruitment of several small nuclear ribonucleoproteins (snRNPs) involved in the splicing of U12-type introns. The pre-mRNA is depicted by a red ribbon, and the U12 small nuclear RNA (snRNA) by a green ribbon, with bases and Watson-Crick base pairs represented as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; the proteins are shown as gold ribbons. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

October 2025

Human tRNA splicing endonuclease (TSEN) complex bound to pre-tRNAArg (PDB id: 7UXA; Hayne CK, Butay KJ, Stewart ZD, Krahn JM, Perera L, Williams JG, Petrovitch RM, Deterding LJ, Matera AG, Borgnia MJ, Stanley RE. 2023. Structural basis for pre-tRNA recognition and processing by the human tRNA splicing endonuclease complex. Nat Struct Mol Biol 30: 824–833). Cryo-EM structure of the TSEN protein assembly with pre-tRNAArg provides insights into the recognition and splicing of an intron that must be removed from the pre-tRNA before translation. The pre-tRNAArg is depicted by a red ribbon, with bases and Watson-Crick base pairs represented as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; the TSEN subunits are shown as gold ribbons. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

September 2025

Systemic RNA interference defective protein 1 (SID1) in complex with dsRNA (PDB id: 8XC1; Wang R, Cong Y, Qian D, Yan C, Gong D. 2024. Structural basis for double-stranded RNA recognition by SID1. Nucleic Acids Res 52: 6718–6727). The cryo-EM structure provides a major step towards understanding the mechanism of dsRNA recognition by SID1, involving extensive interactions between basic amino-acid residues and the sugar-phosphate backbone. The dsRNA chains are depicted by red, green, blue, and yellow ribbons, with bases and Watson-Crick base pairs represented as color-coded blocks and minor-groove edges colored white: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; SID1 is shown by a gold ribbon. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

August 2025

Complex of arginyl-tRNA-protein transferase 1 (ATE1) with tRNA^Arg and a short peptide substrate (PDB id: 8UAU; Lan X, Huang W, Kim SB, Fu D, Abeywansha T, Lou J, Balamurugan U, Kwon YT, Ji CH, Taylor DJ, Zhang Y. 2024. Oligomerization and a distinct tRNA-binding loop are important regulators of human arginyl-transferase function. Nat Commun 15: 6350). The ATE1 homodimer dissociates upon binding the peptide and forms a loop that wraps around tRNA^Arg. The tRNA^Arg is depicted by a red ribbon, with bases and Watson–Crick base pairs represented as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; ATE1 is shown by a gold ribbon and the peptide by a white ribbon. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

July 2025

Structure of endoribonuclease P (RNase P) in complex with pre-tRNA^His-Ser (PDB id: 8CBK; Meynier V, Hardwick SW, Catala M, Roske JJ, Oerum S, Chirgadze DY, Barraud P, Yue WW, Luisi BF, Tisné C. 2024. Structural basis for human mitochondrial tRNA maturation. Nat Commun 15: 4683). The structure reveals the first step of human mitochondrial tRNA maturation by RNase P, processing the 5′-leader of pre-tRNA. The RNA is depicted by a red ribbon, with bases and Watson-Crick base pairs represented as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; the protein assembly is shown by the gold ribbons. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

June 2025

Structure of a group II intron ribonucleoprotein in the pre-ligation state (PDB id: 8T2R; Xu L, Liu T, Chung K, Pyle AM. 2023. Structural insights into intron catalysis and dynamics during splicing. Nature 624: 682–688). The pre-ligation complex of the Agathobacter rectalis group II intron reverse transcriptase/maturase with intron and 5′-exon RNAs makes it possible to construct a picture of the splicing active site. The intron is depicted by a green ribbon, with bases and Watson-Crick base pairs represented as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; the 5′-exon is shown by white spheres and the protein by a gold ribbon. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

May 2025

Complex of terminal uridylyltransferase 7 (TUT7) with pre-miRNA and Lin28A (PDB id: 8OPT; Yi G, Ye M, Carrique L, El-Sagheer A, Brown T, Norbury CJ, Zhang P, Gilbert RJ. 2024. Structural basis for activity switching in polymerases determining the fate of let-7 pre-miRNAs. Nat Struct Mol Biol 31: 1426–1438). The RNA-binding pluripotency factor LIN28A invades and melts the RNA and affects the mechanism of action of the TUT7 enzyme. The RNA backbone is depicted by a red ribbon, with bases and Watson-Crick base pairs represented as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; TUT7 is represented by a gold ribbon and LIN28A by a white ribbon. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

April 2025

Cryo-EM structure of the pre-B complex (PDB id: 8QP8; Zhang Z, Kumar V, Dybkov O, Will CL, Zhong J, Ludwig SE, Urlaub H, Kastner B, Stark H, Lührmann R. 2024. Structural insights into the cross-exon to cross-intron spliceosome switch. Nature 630: 1012–1019). The pre-B complex is thought to be critical in the regulation of splicing reactions. Its structure suggests how the cross-exon and cross-intron spliceosome assembly pathways converge. The U4, U5, and U6 snRNA backbones are depicted respectively by blue, green, and red ribbons, with bases and Watson-Crick base pairs shown as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; the proteins are represented by gold ribbons. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

February 2025

Structure of the Hendra henipavirus (HeV) nucleoprotein (N) protein-RNA double-ring assembly (PDB id: 8C4H; Passchier TC, White JB, Maskell DP, Byrne MJ, Ranson NA, Edwards TA, Barr JN. 2024. The cryoEM structure of the Hendra henipavirus nucleoprotein reveals insights into paramyxoviral nucleocapsid architectures. Sci Rep 14: 14099). The HeV N protein adopts a bi-lobed fold, where the N- and C-terminal globular domains are bisected by an RNA binding cleft. Neighboring N proteins assemble laterally and completely encapsidate the viral genomic and antigenomic RNAs. The two RNAs are depicted by green and red ribbons. The U bases of the poly(U) model are shown as cyan blocks. Proteins are represented as semitransparent gold ribbons. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

January 2025

Structure of the helicase and C-terminal domains of Dicer-related helicase-1 (DRH-1) bound to dsRNA (PDB id: 8T5S; Consalvo CD, Aderounmu AM, Donelick HM, Aruscavage PJ, Eckert DM, Shen PS, Bass BL. 2024. Caenorhabditis elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA. eLife 13: RP93979. Cryo-EM structures of Dicer-1 in complex with DRH-1, RNAi deficient-4 (RDE-4), and dsRNA provide mechanistic insights into how these three proteins cooperate in antiviral defense. The dsRNA backbone is depicted by green and red ribbons. The U-A pairs of the poly(A)·poly(U) model are shown as long rectangular cyan blocks, with minor-groove edges colored white. The ADP ligand is represented by a red block and the protein by a gold ribbon. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

Moreover, the following 30 [12(2021) + 12(2022) + 6(2023)] cover images of the RNA Journal were generated by the NAKB (nakb.org).

Cover image provided by the Nucleic Acid Database (NDB)/Nucleic Acid Knowledgebase (NAKB; nakb.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

Curves+ vs 3DNA

While browsing Nucleic Acids Research recently, I noticed the paper titled Conformational analysis of nucleic acids revisited: Curves+ by Dr. Lavery et al. I read it through carefully during the weekend and played around with the software. Overall, I was fairly impressed, and also happy to see that “It [Curves+] adopts the generally accepted reference frame for nucleic acid bases and no longer shows any significant difference with analysis programs such as 3DNA for intra- or inter-base pair parameters.”

Anyone who has ever worked on nucleic acid structures (especially DNA) should be familiar with Curves, an analysis program that has been widely used over the past twenty years. Only in recent years has 3DNA become popular. By and large, though, it is my opinion that 3DNA and Curves are constructive competitors in nucleic acid structure analysis with complementary functionality. As I put it six years ago, before the 13th Conversation at Albany: “Curves has special features that 3DNA does not want to repeat/compete (e.g. global parameters, groove dimension parameters). Nevertheless, we provide an option in a 3DNA utility program (find_pair) to generate input to Curves directly from a PDB data file” on June 6, 2003, and emphasized again on June 09, 2003: “We also see Curves unique in defining global parameters, bending analysis and groove dimensions.” 3DNA’s real strength, as demonstrated in our 2008 Nature Protocols paper, lies in its integrated approach that combines nucleic acid structure analysis, rebuilding, and visualization into a single software package (see image below).

3DNA v2 composite image

Now the nucleic acid structure community is blessed with the new Curves+, which “is algorithmically simpler and computationally much faster than the earlier Curves approach”, yet still provides its ‘hallmark’ curvilinear axis and “a full analysis of groove widths and depths”. When I read the text, I especially liked the INTRODUCTION section, which provides a nice summary of relevant background information on nucleic acid conformational analysis. An important feature of Curves+ is its integration of the analysis of molecular dynamics trajectories. In contrast, 3DNA lacks direct support in this area (even though I know of such applications from questions posted on the 3DNA forum), mostly due to the fact that I am not an ‘energetic’ person. Of special note is a policy-related advantage Curves+ has over 3DNA: Curves+ is distributed freely, and with source code available. On the other hand, due to Rutgers’ license constraints and various other (undocumented) reasons, 3DNA users are still having difficulty in accessing 3DNA v2.0 I compiled several months ago!

It is worth noting that the major differences in slide (+0.47 Å) and x-displacement (+0.77 Å) in Curves+ vs the old Curves (~0.5 Å and ~0.8 Å, respectively) are nearly exactly those uncovered a decade ago in Resolving the discrepancies among nucleic acid conformational analyses [Lu and Olson (1999), J. Mol. Biol., 285(4), 1563-75]:

Except for Curves, which defines the local frame in terms of the canonical B-DNA fiber structure (Leslie et al., 1980), the base origins are roughly coincident in the different schemes, but are significantly displaced (~0.8 Å along the positive x-axis) from the Curves reference. As illustrated below, this offset gives rise to systematic discrepancies of ~0.5 Å in slide and ~0.8 Å in global x-displacement in Curves compared with other programs, and also contributes to differences in rise at kinked steps. (p. 1566)

Please note that Curves+ has introduced new name list variables — most notably, lib= — and other subtle format changes, thus rendering the find_pair generated input files (with option ‘-c’) no longer valid. However, it would be easy to manually edit the input file to make it work for Curves+, since the most significant part — i.e., specifying paired nucleotides — does not change. Given time and upon user request, however, I would consider to write a new script to automate the process.

Overall, it is to the user community’s advantage to have both 3DNA and Curves+ or a choice between the two programs, and I am more than willing to build a bridge between them to make users’ lives easier.

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X3DNA-DSSR: a resource for structural bioinformatics of nucleic acids(An NIGMS National Resource supported by NIH grant R24GM153869)

X3DNA-DSSR: a resource for structural bioinformatics of nucleic acids
(An NIGMS National Resource supported by NIH grant R24GM153869)